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replay: Use swh.model.from_disk.Directory.collect

Antoine Lambert requested to merge generated-differential-D8693-source into generated-differential-D8693-target

Instead of maintaining a set of modified paths for each replayed revision, use the swh.model.from_disk.Directory.collect method which performs the same task by returning added or modified contents and directories since the last collect operation.

Migrated from D8693 (view on Phabricator)

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